SLC44A3

solute carrier family 44 member 3, the group of Solute carrier family 44

Basic information

Region (hg38): 1:94820341-94895246

Links

ENSG00000143036 ∙ NCBI:126969 ∙ ∙ HGNC:28689 ∙ Uniprot:Q8N4M1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC44A3 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC44A3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	0

Variants in SLC44A3

This is a list of pathogenic ClinVar variants found in the SLC44A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-94820949-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-94820962-G-C		not specified	Uncertain significance (Sep 01, 2021)
1-94821013-A-T		not specified	Uncertain significance (Nov 14, 2023)
1-94824497-T-A		not specified	Uncertain significance (Mar 04, 2024)
1-94824511-T-C		not specified	Uncertain significance (Feb 17, 2022)
1-94824529-G-A		not specified	Likely benign (Jun 05, 2023)
1-94824530-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-94827562-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-94827624-G-T		not specified	Uncertain significance (Dec 19, 2023)
1-94837847-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-94840004-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-94842068-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-94842095-G-T		not specified	Uncertain significance (Sep 26, 2023)
1-94842107-G-A		not specified	Uncertain significance (Jan 27, 2022)
1-94842123-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-94845281-G-A		not specified	Uncertain significance (Sep 14, 2023)
1-94845287-C-G		not specified	Uncertain significance (Feb 28, 2023)
1-94845290-G-A		not specified	Likely benign (Jul 20, 2021)
1-94845402-T-C		not specified	Uncertain significance (Sep 21, 2023)
1-94857391-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-94864760-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-94864778-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-94891209-A-G		not specified	Uncertain significance (Jun 09, 2022)
1-94891229-A-G		not specified	Likely benign (Dec 15, 2022)
1-94892396-C-T		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC44A3	protein_coding	protein_coding	ENST00000271227	15	74905

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.60e-27	0.0000341	125551	0	197	125748	0.000784

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.994	291	343	0.849	0.0000172	4272
Missense in Polyphen		86	105.11	0.81817		1408
Synonymous	0.965	125	139	0.896	0.00000784	1249
Loss of Function	-0.669	38	33.8	1.12	0.00000177	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00294	0.00293
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.00340	0.00332
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000575	0.000571
Middle Eastern	0.00340	0.00332
South Asian	0.000441	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Choline metabolism in cancer - Homo sapiens (human);Metabolism of lipids;Amine compound SLC transporters;Metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;Synthesis of PC;SLC-mediated transmembrane transport;Transport of small molecules;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0935

Intolerance Scores

• loftool: 0.996
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.25

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.219
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.701

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc44a3

Gene ontology

• Biological process: phosphatidylcholine biosynthetic process;choline transport;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;choline transmembrane transporter activity